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Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

ABSTRACT: The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris A 2.65-Å resolution structure of the RC-LH114-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16-subunit LH1 ring. Comparison of these structures provides insights into quinone dynamics within RC-LH1 complexes, including a previously unidentified conformational change upon quinone binding at the RC QB site, and the locations of accessory quinone binding sites that aid their delivery to the RC. The structurally unique protein-W prevents LH1 ring closure, creating a channel for accelerated quinone/quinol exchange.

SUBMITTER: Swainsbury DJK

PROVIDER: S-EPMC7806223 | biostudies-literature | 2021 Jan

REPOSITORIES: biostudies-literature

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Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

Swainsbury David J K DJK Qian Pu P Jackson Philip J PJ Faries Kaitlyn M KM Niedzwiedzki Dariusz M DM Martin Elizabeth C EC Farmer David A DA Malone Lorna A LA Thompson Rebecca F RF Ranson Neil A NA Canniffe Daniel P DP Dickman Mark J MJ Holten Dewey D Kirmaier Christine C Hitchcock Andrew A Hunter C Neil CN

Science advances 20210113 3

The reaction-center light-harvesting complex 1 (RC-LH1) is the core photosynthetic component in purple phototrophic bacteria. We present two cryo-electron microscopy structures of RC-LH1 complexes from Rhodopseudomonas palustris A 2.65-Å resolution structure of the RC-LH114-W complex consists of an open 14-subunit LH1 ring surrounding the RC interrupted by protein-W, whereas the complex without protein-W at 2.80-Å resolution comprises an RC completely encircled by a closed, 16- ...[more]

PMID: 33523887

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Project description:Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R. palustris genomes.

Project description:A series of oligothiophene bis(dioxolene) complexes, SQ-Thn-SQ (SQ = S = ½TpCum,MeZnII(3-tert-butyl-orthosemiquinonate); TpCum,Me = tris(5-cumenyl-3-methylpyrazolyl)borate anion) have been synthesized, structurally characterized, and studied as a function of the number of thiophene bridging units, n (n = 0-3) using a combination of variable-temperature (VT) electronic absorption and EPR spectroscopies, and VT magnetic susceptibility measurements. The thiophene bridge bond lengths determined by X-ray crystallography display dramatic differences across the SQ-Thn-SQ series. Bridge bond deviation values (Σ|Δi|) display a progressive change in the nature of the bridge fragment bonding as the number of thiophene groups increases, with quinoidal bridge character for n = 1 (SQ-Th-SQ) and biradical character with "aromatic" bridge bond lengths for n = 3 (SQ-Th3-SQ). Remarkably, for n = 2 (SQ-Th2-SQ) the nature of the bridge fragment is intermediate between quinoid and biradical aromatic, which we describe as having open-shell character as opposed to biradicaloid since the open-shell biradical configuration does not have the correct symmetry to mix with the quinoidal ground-state configuration. This bridge bonding character is reflected in the energies of the lowest lying open-shell states for these three molecules. The SQ-Th-SQ molecule is diamagnetic at all temperatures studied, and we provide evidence for SQ-SQ antiferromagnetic exchange coupling and population of triplet states in SQ-Th2-SQ and SQ-Th3-SQ, with JSQ-SQ(ave) = -279 cm-1 (VT EPR/electronic absorption/magnetic susceptibility) and JSQ-SQ = -117 cm-1 (VT EPR/electronic absorption/magnetic susceptibility), respectively. The results have been interpreted in the context of state configurational mixing within a simplified 4-electron, 3-orbital model that explicitly contains contributions of a bridge fragment. Variable-temperature spectroscopic- and magnetic susceptibility data are consistent with two low-lying open-shell states for SQ-Th3-SQ, but three low-lying states (one closed-shell and two open-shell) for SQ-Th2-SQ. This model provides a simple symmetry-based framework to understand the continuum of electronic and geometric structures of this class of molecules as a function of the number of thiophene units in the bridge.

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Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

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Structures of <i>Rhodopseudomonas palustris</i> RC-LH1 complexes with open or closed quinone channels.

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Structures of Rhodopseudomonas palustris RC-LH1 complexes with open or closed quinone channels.

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Structures of &lt;i&gt;Rhodopseudomonas palustris&lt;/i&gt; RC-LH1 complexes with open or closed quinone channels.

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Structures of <i>Rhodopseudomonas palustris</i> RC-LH1 complexes with open or closed quinone channels.